issue #327 change Alignment usingTipLikelihoods to protected
issue #327 change Alignment usingTipLikelihoods to protected

Anaphory/beast2,Anaphory/beast2,CompEvol/beast2,tgvaughan/beast2,Anaphory/beast2,CompEvol/beast2,Anaphory/beast2,tgvaughan/beast2,tgvaughan/beast2,tgvaughan/beast2,CompEvol/beast2,CompEvol/beast2